The MHA has asked for the government's top cyber security experts for help.

The Ministry of Home Affairs (MHA) on Wednesday called in India's top cyber security experts, Computer Emergency Response System (CERT-In), suspecting their systems have been hacked.

The move comes after an embarassing episode in which the MHA cancelled the mysteriously "renewed" licenses of three NGOs which had lost licenses to receive foreign funds. The ministry grants permission and supervises usage of foreign donations, and this is the second time in six months when licenses to receive foreign funds have been renewed erroneously. As per the MHA's own admission, the license of at least one more NGO was earlier renewed similarly.

Apart from a cyber security check, the ministry also has ordered an audit and manual review of all 13,000 licenses that were renewed this year.

In this case, the three NGOs whose licenses were renewed are Greenpeace, and Teesta Setalvad's Sabrang Trust and Citizen for Justice and Peace (CJP). According to the Greenpeace India's executive director Ravi Chellam, the NGO's license was renewed with effect from 1 November this year. All three NGOs were renewed for five years, but the MHA has now said that these orders stand "null and void". When cancelling their licenses, the MHA had claimed funds received by these three NGOs from foreign donors were misused. In particular, Greenpeace was accused of using foreign donations to fuel protest against civil nuclear plants in India. Setalvad's NGOs were accused of diverting foreign donations for "personal gains." CJP was allowed to receive funds but has to take to prior permission from the MHA. Both Greenpeace and Teesta Setalvad had objected.

A license to receive foreign funds under Foreign Contribution Regulation Act (FCRA)--that governs who can receive foreign donations and how such funds are used--is now issued through a new online system. The system was introduced by the Modi government to ensure transparency. Use of foreign funds is also monitored by same online system.

The suspicion of possible breach of cyber security of the MHA comes at a time when the Modi government is pushing for electronic payments. "We cannot rule-out a cyber breach. We aren't sure just how many NGOs--who shouldn't have a license--have been issued with a license. Also, this second time that in a few months when the online systems seems to have failed," a top MHA official told HuffPost India.

Earlier in August 2016, the MHA the license to receive foreign funds of Islamic Research Foundation (IRF) of controversial preacher Zakir Naik was renewed even when he was being investigated for allegedly motivating terrorist. It is alleged that Naik's inflammatory speeches motivated gunmen who stormed an upmarket café in Dhaka killing 29 people. Bangladesh had officially taken up the issue and formal investigation against Naik was launched in India.

Interestingly, the licenses of these three NGOs too were renewed in August 2016. But the fact that licenses were renewed came to light only in November.

After Naik's license was renewed three officials including a senior joint secretary were suspended. The ministry had then said that the renewal was an "oversight" which had been taken seriously.